Bioinformatics World FAQ Center

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FAQ Index

last modified Sep 20 2006 at 14:32
last complete check for broken links: August 22, 2006

The purpose of this page is to provide step-by-step descriptions how to solve specific problems using bioinformatics tools and databases. It is intended as a constantly growing knowledge database covering many topics from general sequence similarity search, over protein and expression databases, to advanced fields like 3D structures or comparative genomics. The subtopics are similar to those in the main index so you can easily find cross-references. If you know a question of general interest which should be included at this site you are strongly encouraged to let me know.

Total number of FAQs: 86

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Top Sites TOP SITES
        TOP1...explore the world of bioinformatics as a novice in the field ? (last update Feb. 7, 2006)
        TOP2...find concise literature describing databases and web servers currently available ? (last update Feb. 7, 2006)
        TOP3...get a quick overview of the services provided by the major bioinformatics institutes ? (last update Mar. 20, 2006)

Data Integration DATA INTEGRATION
        DAT1...get a quick, yet comprehensive overview of data concerning my gene / protein of interest ? (last update Aug. 26, 2005)
        DAT2...get the full-length sequence and annotation from an EST sequence or accession number ? (last update Sep. 14, 2005)  
        DAT3...retrieve a large number of sequences and write one common FASTA sequence file ? -> see RET3 !
        DAT4...know which genes of a specific dataset are associated with a disease ? -> see GENOM5 !
        DAT5...know all genes associated with cardiovascular diseases having a described polymorphism in the promoter region ? -> see GENOM7 !
        DAT6...convert a list of IDs (like microarray probe IDs) into other IDs (like gene names) ? (last update Jun. 27, 2006)
        DAT7...see the functions and pathways where my gene set of interest is involved ? -> see PATH1 !
        DAT8...produce a general annotation table for a gene set of interest ? (last update Dec. 21, 2005)
                     
Literature LITERATURE
        LIT1...know in which publications my own papers are cited ? (last update Feb. 7, 2006)
        LIT2...see if patents exist which are related to a molecule of interest ? (last update Feb. 7, 2006)
        LIT3...perform a PubMed query using automatically all synonyms of my gene name of interest ? (last update Feb. 23, 2006)
        LIT4...see the authors which are most active in a specific field and their preferred journals ? (last update Feb. 23, 2006) 
        
Seq Ret SEQUENCE RETRIEVAL
        RET1...know all proteins which contain a certain domain or motif in their sequence ? (last update May 15, 2006)
        RET2...get all proteins from endothelial cells involved in inflammation (SRS and GO approaches) ?  (last update Feb. 9, 2006)
        RET3...retrieve a large number of sequences (including whole-genome datasets) and write one common FASTA sequence file ? (last update Mar. 3, 2006)
        RET4...get all transcription factors expressed in certain tissues or cell types ?  (last update Feb. 9, 2006)
        RET5...get all N-glycosylated proteins localized in the endoplasmic reticulum ?  (last update Aug. 26, 2005)
        RET6...get all human proteins present in Drosophila but not in C. elegans ? -> see GENOM4 !
        RET7...know all genes associated with cardiovascular diseases having a described polymorphism in the promoter region ? -> see GENOM7 !
        RET8...get the promoter/protein sequences of all proteins homologous to my query within a certain species ?  (last update Jun. 2, 2005)   
        RET9...know the genes and drugs related to diseases like atherosclerosis ? -> see CHEM2 !   
        RET10...get all human transcription factors involved in inflammation ? -> see PATH4 !      
        RET11...download the gene lists of individual pathways for further data analysis ? -> see PATH7 !            
                            
Seq Sim SEQUENCE SIMILARITY
        SIM1...search databases with a batch of sequences using BLAST or other tools ? (last update May 5, 2006)
        SIM2...search databases using short sequences like oligos and peptides ? (last update May 5, 2006)
        SIM3...produce a multiple sequence alignment from a group of related sequences ? (last update Sep. 19, 2006)
        SIM4...produce sequence logos from a group of related sequences ? (last update May 9, 2006)
        SIM5...test the specificity of a PCR primer pair within a genome ? -> see DNA4 !
        SIM6...match my query sequence very quickly with a whole-genome assembly ? (last update May 5, 2006)
        SIM7...search for (also distant) orthologs/homologs of my gene/protein of interest ? -> see GENOM2 !     
                                
Nuc DNA
        DNA1...design PCR or sequencing primers from my query sequence ? (last update May 12, 2005)
        DNA2...design degenerate primers to fish related protein family members ? (last update Feb. 24, 2004)
        DNA3...design primers in least conserved regions of protein families ? (last update Feb. 24, 2004)
        DNA4...test the specificity of a PCR primer pair within a genome ? (last update Sep. 6, 2004)
        DNA5...translate a DNA sequence and see both DNA and protein sequence in the output ? (last update Sep. 8, 2005)
                                      
Nuc RNA
        RNA1...detect regulatory elements in UTRs (UnTranslated Regions) in a whole-genome approach ? (last update Sep. 7, 2005)
        RNA2...get a structural prediction for the 3'-UTR sequence of my RNA of interest ? (last update Sep. 6, 2005)     
        RNA3...get detailed information about a regulatory microRNA called miR-16 ? (last update Oct. 31, 2005)      
        RNA4...predict the potential targets of a microRNA like miR-16 ? (last update Nov. 2, 2005)    
        RNA5...predict if a specific mRNA of interest may be the target of microRNAs ? (last update Nov. 2, 2005)         
                                           
Gene Analysis GENES
        GEN1...know if a stretch of genomic sequence contains a potential promoter region ? (last update May 28, 2006)
        GEN2...know which transcription factor binding sites, TF modules, or user-defined patterns and profiles are present in my promoter region ? (last update May 30, 2006)
        GEN3...know if there are repetitive elements in my DNA sequence ? (last update Nov. 18, 2005)
        GEN4...know which promoters or enhancers in a whole genome contain a binding site for a single or a combination of transcription factors (Motif Matching; Module Scanners) ? (last update Mar. 14, 2006)
        GEN5...know which regulatory elements are common in a set of promoter sequences and check if these motifs are known transcription factor binding sites (Motif Discovery) ? (last update Mar. 30, 2006)
        GEN6...quickly extract potential promoter sequences for a batch of human genes ? (last update May 29, 2006)
        GEN7...quickly see the binding site profiles of individual transcription factors ? (last update May 18, 2005)
        GEN8...detect regulatory elements in UTRs (UnTranslated Regions) in a whole-genome approach ? -> see RNA1 !
        GEN9...get the promoter/protein sequences of all proteins homologous to my query within a certain species ? -> see RET8 !
        GEN10...check how often a specific motif is present in a randomly generated sequence set ? (last update Jun. 3, 2005) 
                              
Genomics GENOMICS
        GENOM1...scan my gene (set) of interest for the presence of SNPs (Single Nucleotide Polymorphisms)? (last update Feb. 22, 2006)
        GENOM2...search for (also distant) orthologs/homologs of my gene/protein of interest ? (last update May 5, 2006)
        GENOM3...see which regulatory elements are conserved in a set of orthologous promoters (Phylogenetic Footprinting) ? -> see GEN5 !   
        GENOM4...get all human proteins present in Drosophila but not in C. elegans ? (last update Apr. 14, 2004)   
        GENOM5...know which genes of a specific dataset are associated with a disease ? (last update Jun. 7, 2005)
        GENOM6...identify Conserved Non-coding Sequences (CNS) and conserved transcription factor binding sites in large genomic regions via comparative genomics ? (last update Mar. 14, 2006)
        GENOM7...know all genes associated with cardiovascular diseases having a described polymorphism in the promoter region ? (last update Jun. 7, 2005)
        GENOM8...know the genes and drugs related to diseases like atherosclerosis ? -> see CHEM2 !     
        GENOM9...analyze the expression of a gene set of interest in cancer tissues ? (last update Feb. 13, 2006)        
        GENOM10...determine the expression profiles of normal vs. cancer tissues ? (last update Feb. 13, 2006)    
                                              
Human Genome THE HUMAN GENOME
        HUMGEN1...know which way is the best to access the human genome data ? (last update Mar. 2, 2006)
                
Other Genomes OTHER GENOMES
        OTHGEN1...know which way is the best to access the mouse genome data ? (last update Mar. 2, 2006)
                
Expression EXPRESSION
        EXP1...know the best access to expression data for a gene of interest ? (last update Mar. 3, 2006)
        EXP2...know which available microarrays contain a gene or a whole gene set of interest ? (last update Aug. 30, 2005)
        EXP3...know which published microarray experiments contain data of my gene of interest ? (last update Aug. 30, 2005)
        EXP4...identify genes with expression patterns similar to my gene of interest ? (last update Jun. 1, 2004)
        EXP5...query microarray data not by gene name but by the "nature of the experiment" ? (last update Nov. 11, 2004)
        EXP6...perform in silico expression profiling in the field of endothelial cell biology ? (last update Jun. 14, 2005)
        EXP7...perform clustering analyses of microarray data ? (last update Jun. 18, 2006)
        EXP8...get all proteins from endothelial cells involved in inflammation (SRS and GO approaches) ? -> see RET2 !   
        EXP9...submit my own microarray data to a public database ? (last update Jan. 3, 2006)
        EXP10...compare the expression of my gene of interest in B-cells, T-cells, monocytes, and dendritic cells ? (last update Aug. 20, 2004)
        EXP11...get a "virtual multiple tissue Northern blot" of my gene of interest ? (last update Mar. 3, 2006)
        EXP12...know which genes are expressed in fetal brain 6 times higher than in adult brain ? (last update Aug. 20, 2004)
        EXP13...compare two different microarray platforms and see which genes are represented on both of them ? (last update Aug. 31, 2005)
        EXP14...compare a list of upregulated genes from one microarray experiment with one or more other experiments ? (last update Aug. 31, 2005)
        EXP15...know if alternative transcripts of a gene of interest are expressed in different tissues or in different diseases ? (last update Sep. 16, 2005)
        EXP16...generate contig sequences from a set of ESTs while considering alternative splicing  ? (last update Sep. 16, 2005)
        EXP17...analyze the expression of a gene set of interest in cancer tissues ? -> see GENOM9 !
        EXP18...determine the expression profiles of normal vs. cancer tissues ? -> see GENOM10 !
        EXP19...determine the reliability of individual SAGE tags for expression analysis of a specific gene ? (last update Feb. 10, 2006)
        EXP20...get in situ microscopy images of RNA tissue localization and expression intensity ? (last update Mar. 2, 2006)
        EXP21...get RT-PCR, Northern Blot, and Western Blot expression data ? (last update Mar. 3, 2006)
                                              
Proteins PROTEINS
        PROT1...know which domains and motifs can be found in my protein query sequence ? (last update May 15, 2006)
        PROT2...know all proteins which contain a certain domain or motif in their sequence ? -> see RET1 !
        PROT3...get a structural prediction for my protein of interest ? (last update Jul. 21, 2005)
        PROT4...know which protein family my protein belongs to ? -> see GENOM2 !
        PROT5...screen a batch of protein sequences for transmembrane regions ? (last update Mar. 30, 2006)
        PROT6...predict the subcellular localization or retrieve experimental localization data of my protein of interest ? (last update Dec. 6, 2005) 
        PROT7...know which protein domains are present / overrepresented in my gene set of interest ? (last update Jan. 24, 2006)      
                        
3D 3D STRUCTURES
        STRUC1...know if there are proteins with known 3D structures homologous to my query sequence and if I want to visualize these structures ? (last update May 17, 2006)
        STRUC2...distinguish ordered (globular) and disordered (unstructured) regions in my protein of interest ? (last update Nov. 17, 2003) 

Expression PATHWAYS, INTERACTIONS, FUNCTIONS
        PATH1...predict the pathways, interactions and functions for a gene set of interest ? (last update Jun. 27, 2006)
        PATH2...get all proteins from endothelial cells involved in inflammation (SRS and GO approaches)? -> see RET2 !   
        PATH3...predict potential protein-protein interactions of my protein of interest? (last update May 15, 2006)
        PATH4...get all human transcription factors involved in inflammation ? (last update Dec. 21, 2005)
        PATH5...know which protein domains are present / overrepresented in my gene set of interest ? -> see PROT7 !   
        PATH6...get detailed information on metabolic pathways, reactions, and compounds ? (last update Feb. 1, 2006)
        PATH7...download the gene lists of individual pathways for further data analysis ? (last update Apr. 24, 2006)
                      
Expression CHEMINFORMATICS
        CHEM1...know the structure and function of anti-inflammatory drugs like aspirin or celebrex ? (last update Aug. 23, 2005) 
        CHEM2...know the genes and drugs related to diseases like atherosclerosis ? (last update Aug. 23, 2005)  
                       
Graphics GRAPHICAL TOOLS
        GRAPH1...visualize conserved sequences in a multiple sequence alignment ? (last update May 9, 2006)
        
Various VARIOUS TOOLS
        VAR1...quickly convert sequence formats from different applications ? (last update Jun. 20, 2002)
        VAR2...check how often a specific motif is present in a randomly generated sequence set ?  -> see GEN10 !            
        VAR3...convert a list of IDs (like microarray probe IDs) into other IDs (like gene names) ?  -> see DAT6 !                                             
                        
Bioinformatics BIOINFORMATICS DEVELOPMENT
        BIO1...get access to discussion forums dealing with bioinformatics topics ? (last update Feb. 7, 2006)
           
                           
Informatics INFORMATICS
        INFO1...quick-search all of the "Bioinformatics World" pages for a certain tool or database ? (last update Mar. 1, 2006)
              

Bioinformatics World was developed by Herbert Mayer, Medical University of Vienna, Austria (2001-2006)